arthurpsm...@gmail.com has uploaded a new change for review.
https://gerrit.wikimedia.org/r/245591
Change subject: Added a wikidata-based "chart of the nuclides" under the
periodic table app (link to /nuclides)
......................................................................
Added a wikidata-based "chart of the nuclides" under the periodic table app
(link to /nuclides)
Change-Id: I0a3fe4c20f6442f951cd54a1024334283dd9aaeb
---
M app.py
A nuclides.py
A static/nuclides.css
A templates/nuclides.html
A units.py
5 files changed, 386 insertions(+), 1 deletion(-)
git pull ssh://gerrit.wikimedia.org:29418/labs/tools/ptable
refs/changes/91/245591/1
diff --git a/app.py b/app.py
index 00ad692..a22ff5c 100644
--- a/app.py
+++ b/app.py
@@ -20,6 +20,7 @@
from flask.json import JSONEncoder
import chemistry
+import nuclides
class CustomJSONEncoder(JSONEncoder):
@@ -34,11 +35,14 @@
# May be set to chemistry.ApiElementProvider (slower, but more up-to-date)
element_provider_class = chemistry.WdqElementProvider
+nuclide_provider_class = nuclides.WdqNuclideProvider
-fake_globals = {'isinstance': isinstance}
+fake_globals = {'isinstance': isinstance, 'sorted': sorted}
for key in ('EmptyCell', 'UnknownCell', 'ElementCell', 'IndicatorCell'):
fake_globals[key] = getattr(chemistry, key)
+for key in ('NoneCell', 'NuclideCell'):
+ fake_globals[key] = getattr(nuclides, key)
@app.before_request
def set_language():
@@ -49,6 +53,7 @@
if not app.language:
app.language = 'en'
app.element_provider = element_provider_class(app.language)
+ app.nuclide_provider = nuclide_provider_class(app.language)
@app.route('/')
@@ -59,6 +64,14 @@
incomplete=incomplete, **fake_globals)
+@app.route('/nuclides')
+def nuclides():
+ """Render the chart of the nuclides."""
+ nuclides, table, incomplete = app.nuclide_provider.get_table()
+ return render_template('nuclides.html', table=table,
+ incomplete=incomplete, **fake_globals)
+
+
@app.route('/license')
def license():
"""Render the license page."""
diff --git a/nuclides.py b/nuclides.py
new file mode 100644
index 0000000..9f13c35
--- /dev/null
+++ b/nuclides.py
@@ -0,0 +1,215 @@
+import json
+import operator
+from units import time_quantity_in_seconds
+from urllib import urlencode
+from urllib2 import urlopen
+from collections import defaultdict
+
+try:
+ from functools import ttl_cache
+except ImportError:
+ from cachetools import ttl_cache
+
+
+# cachetools does not support maxsize=None
+@ttl_cache(maxsize=20, ttl=21600)
+def get_json_cached(url, data):
+ """The information is cached for 6 hours."""
+ return json.load(urlopen(url, data))
+
+
+def get_json(url, data):
+ return get_json_cached(url, urlencode(data))
+
+
+class NuclideProvider(object):
+ """Base class for nuclide providers."""
+
+ WD_API = 'http://www.wikidata.org/w/api.php'
+ API_LIMIT = 50
+ WDQ_API = 'http://wdq.wmflabs.org/api'
+
+ def __init__(self, language):
+ self.language = language
+
+ @classmethod
+ def get_entities(cls, ids, **kwargs):
+ entities = {}
+ query = dict(action='wbgetentities', format='json', **kwargs)
+ for index in range(0, len(ids), cls.API_LIMIT):
+ query['ids'] = '|'.join(ids[index:index + cls.API_LIMIT])
+ new_entities = get_json(cls.WD_API, query).get('entities', {})
+ entities.update(new_entities)
+ return entities
+
+ def iter_good(self):
+ iterator = iter(self)
+ while True:
+ try:
+ yield next(iterator)
+ except StopIteration:
+ raise
+
+ def get_table(self):
+ table = {}
+ nuclides = []
+ incomplete = []
+ lastanum = -1
+ lastnnum = -1
+ for nuclide in self.iter_good():
+ if nuclide.atomic_number is not None and nuclide.neutron_number is
not None:
+ if nuclide.atomic_number > lastanum:
+ lastanum = nuclide.atomic_number
+ if nuclide.neutron_number > lastnnum:
+ lastnnum = nuclide.neutron_number
+ if nuclide.atomic_number not in table:
+ table[nuclide.atomic_number] = {}
+ table[nuclide.atomic_number][nuclide.neutron_number] =
nuclide
+ nuclides.append(nuclide)
+ else:
+ incomplete.append(nuclide)
+ nuclides.sort(key=operator.attrgetter('atomic_number',
'neutron_number'))
+ for anum in range(0, lastanum+1):
+ if anum not in table:
+ table[anum] = {}
+ for nnum in range(0,lastnnum+1):
+ if nnum in table[anum]:
+ table[anum][nnum].__class__ = NuclideCell
+ else:
+ table[anum][nnum] = NoneCell()
+
+ return nuclides, table, incomplete
+
+
+class WdqNuclideProvider(NuclideProvider):
+ """Load nuclides from Wikidata Query."""
+ def __iter__(self):
+ wdq = self.get_wdq()
+ ids = ['Q%d' % item_id for item_id in wdq['items']]
+ entities = self.get_entities(ids, props='labels|claims',
+ languages=self.language,
languagefallback=1)
+ nuclides = defaultdict(Nuclide)
+ wdq['props'] = defaultdict(list, wdq.get('props', {}))
+ for item_id, datatype, value in
wdq['props'][str(Nuclide.atomic_number_pid)]:
+ if datatype != 'quantity':
+ continue
+ value = value.split('|')
+ if len(value) == 4:
+ value = map(float, value)
+ if len(set(value[:3])) == 1 and value[3] == 1 and value[0] ==
int(value[0]):
+ nuclides[item_id].atomic_number = int(value[0])
+ for item_id, datatype, value in
wdq['props'][str(Nuclide.neutron_number_pid)]:
+ if datatype != 'quantity':
+ continue
+ value = value.split('|')
+ if len(value) == 4:
+ value = map(float, value)
+ if len(set(value[:3])) == 1 and value[3] == 1 and value[0] ==
int(value[0]):
+ nuclides[item_id].neutron_number = int(value[0])
+ for item_id, datatype, value in
wdq['props'][str(Nuclide.decay_mode_pid)]:
+ if datatype != 'item':
+ continue
+ nuclides[item_id].decay_modes.append(value)
+ for item_id, nuclide in nuclides.items():
+ nuclide.item_id = 'Q%d' % item_id
+ for prop in ('atomic_number', 'neutron_number'):
+ if not hasattr(nuclide, prop):
+ setattr(nuclide, prop, None)
+# ?? nuclide.load_data_from_superclasses(subclass_of[item_id])
+ label = None
+ entity = entities.get(nuclide.item_id)
+ if entity and 'labels' in entity and len(entity['labels']) == 1:
+ label = entity['labels'].values()[0]['value']
+ nuclide.label = label
+
+ if entity:
+ claims = entity['claims']
+ instance_prop = 'P%d' % Nuclide.instance_pid
+ if instance_prop in claims:
+ instance_claims = claims[instance_prop]
+ for instance_claim in instance_claims:
+ class_id =
instance_claim['mainsnak']['datavalue']['value']['numeric-id']
+ if class_id == Nuclide.stable_qid:
+ nuclide.classes.append("stable")
+
+ half_life = None;
+ if entity:
+ claims = entity['claims']
+ hlprop = 'P%d' % Nuclide.half_life_pid
+ if hlprop in claims:
+ hl_claims = claims[hlprop]
+ for hl_claim in hl_claims:
+ half_life = time_quantity_in_seconds(hl_claim)
+ nuclide.half_life = half_life
+ if half_life is not None:
+ if (half_life >= 1.0e9):
+ nuclide.classes.append("hl1e9")
+ elif (half_life >= 1.0e6):
+ nuclide.classes.append("hl1e6")
+ elif (half_life >= 1.0e3):
+ nuclide.classes.append("hl1e3")
+ elif (half_life >= 1.0):
+ nuclide.classes.append("hl1e0")
+ elif (half_life >= 1.0e-3):
+ nuclide.classes.append("hl1e-3")
+ elif (half_life >= 1.0e-6):
+ nuclide.classes.append("hl1e-6")
+ elif (half_life >= 1.0e-9):
+ nuclide.classes.append("hl1e9")
+
+ yield nuclide
+
+ @classmethod
+ def get_wdq(cls):
+ pids = [str(getattr(Nuclide, name))
+ for name in ('atomic_number_pid', 'neutron_number_pid',
'decay_mode_pid')]
+ query = {
+ 'q': 'claim[%d:(tree[%d][][%d])] AND noclaim[%d:%d]' %
(Nuclide.instance_pid, Nuclide.isotope_qid, Nuclide.subclass_pid,
Nuclide.instance_pid, Nuclide.isomer_qid),
+ 'props': ','.join(pids)
+ }
+ return get_json(cls.WDQ_API, query)
+
+
+class PropertyAlreadySetException(Exception):
+ """Property already set."""
+
+
+class Nuclide(object):
+
+ props = ('atomic_number', 'neutron_number', 'item_id', 'label',
'half_life', 'decay_modes')
+ atomic_number_pid = 1086
+ neutron_number_pid = 1148
+ half_life_pid = 2114
+ decay_mode_pid = 817
+ instance_pid = 31
+ subclass_pid = 279
+ isotope_qid = 25276 # top-level class under which all isotopes to be found
+ stable_qid = 878130 # id for stable isotope
+ isomer_qid = 846110 # metastable isomers all instances of this
+
+ def __init__(self, **kwargs):
+ self.decay_modes = []
+ for key, val in kwargs.items():
+ if key in self.props:
+ setattr(self, key, val)
+ self.classes = []
+
+ def __setattr__(self, key, value):
+ if (key in self.props and hasattr(self, key) and
+ getattr(self, key) is not None and getattr(self, key) !=
value):
+ raise PropertyAlreadySetException
+ super(Nuclide, self).__setattr__(key, value)
+
+ def __iter__(self):
+ for key in self.props:
+ yield (key, getattr(self, key))
+
+
+class TableCell(object):
+ """A table cell."""
+
+class NuclideCell(Nuclide, TableCell):
+ """A nuclide cell."""
+
+class NoneCell(TableCell):
+ """An empty cell."""
diff --git a/static/nuclides.css b/static/nuclides.css
new file mode 100644
index 0000000..065c856
--- /dev/null
+++ b/static/nuclides.css
@@ -0,0 +1,60 @@
+table#nuclides{
+ border-spacing: 0;
+}
+table#nuclides td {
+ width: 5px;
+ height: 5px;
+ padding: 0;
+ font-size: 5px;
+ text-align: center;
+ overflow: hidden;
+ text-overflow: ellipsis;
+ border: 0px;
+}
+table#nuclides td.empty {
+ background: none;
+}
+
+table#nuclides td.nuclide{
+ background: #e8e8e8;
+}
+
+table#nuclides td.nuclide.stable {
+ background: #000;
+}
+
+table#nuclides td.nuclide.hl1e9 {
+ background: #008;
+}
+
+table#nuclides td.nuclide.hl1e6 {
+ background: #00c;
+}
+
+table#nuclides td.nuclide.hl1e3 {
+ background: #00f;
+}
+
+table#nuclides td.nuclide.hl1e0 {
+ background: #04c;
+}
+
+table#nuclides td.nuclide.hl1e-3 {
+ background: #088;
+}
+
+table#nuclides td.nuclide.hl1e-6 {
+ background: #4c4;
+}
+
+table#nuclides td.nuclide.hl1e-9 {
+ background: #8f8;
+}
+
+table#nuclides td.x_axis {
+ font-size: 5px;
+ transform: rotate(90.0deg);
+}
+table#nuclides td.y_axis {
+ font-size: 5px;
+}
diff --git a/templates/nuclides.html b/templates/nuclides.html
new file mode 100644
index 0000000..90f5379
--- /dev/null
+++ b/templates/nuclides.html
@@ -0,0 +1,69 @@
+{% extends "base.html" %}
+{%- macro wd_url(nuclide) -%}
+ //www.wikidata.org/wiki/{{ nuclide.item_id }}
+{%- endmacro -%}
+{%- macro format_cell(cell) -%}
+ {%- if isinstance(cell, NoneCell) -%}
+ <td class="empty"></td>
+ {%- elif isinstance(cell, NuclideCell) -%}
+ <td title="{{ cell.label }}" class="nuclide {% for class in
cell.classes %} {{ class }}{% endfor %}"> <a href="{{ wd_url(cell)
}}"> </a> </td>
+ {%- else -%}
+ <td></td>
+ {%- endif -%}
+{%- endmacro -%}
+{% block head -%}
+<link rel="stylesheet" type="text/css" href="static/nuclides.css">
+{% endblock %}
+{% block title %}
+Wikidata chart of the nuclides - Wikimedia Tool Labs
+{% endblock %}
+{% block content %}
+<h1>Wikidata chart of the nuclides</h1>
+{% if incomplete %}
+ <h2>Incomplete</h2>
+ <table>
+ <thead>
+ <tr>
+ <th>nuclide</th>
+ <th>atomic number</th>
+ <th>neutron number</th>
+ </tr>
+ </thead>
+ <tbody>
+ {%- for nuclide in incomplete -%}
+ <tr>
+ <td><a href="{{ wd_url(nuclide) }}">{{
nuclide.label }} ({{ nuclide.item_id }})</a></td>
+ <td>{{ nuclide.atomic_number or '?' }}</td>
+ <td>{{ nuclide.neutron_number or '?' }}</td>
+ </tr>
+ {%- endfor -%}
+ </tbody>
+ </ul>
+{% endif %}
+<table id="nuclides">
+ <tr><td>Proton number</td></tr>
+ {%- for anum in sorted(table.keys(),reverse=True) -%}
+ <tr>
+ <td class="y_axis">
+ {%- if anum % 5 == 0 -%}
+ {{ anum }}
+ {%- endif %}
+ </td>
+ {%- for nnum in sorted(table[anum].keys()) -%}
+ {{ format_cell(table[anum][nnum]) }}
+ {%- endfor -%}
+ </tr>
+ {%- endfor -%}
+ <tr>
+ <td> </td>
+ {%- for nnum in sorted(table[0].keys()) -%}
+ <td class="x_axis">
+ {%- if nnum % 5 == 0 -%}
+ {{ nnum }}
+ {%- endif %}
+ </td>
+ {%- endfor -%}
+ </tr>
+ <tr><td colspan="100" align="center">Neutron number</td></tr>
+</table>
+{% endblock %}
diff --git a/units.py b/units.py
new file mode 100644
index 0000000..7e355df
--- /dev/null
+++ b/units.py
@@ -0,0 +1,28 @@
+# time units and their values in multiples of seconds
+time_units= {
+ 11574: 1.0, # second
+ 7727: 60.0, # minute
+ 25235: 3600.0, # hour
+ 573: 86400.0, # day
+ 23387: 604800.0, # week
+ 5151: 2.630e6, # month (average)
+ 1092296: 3.156e7, # year (annum)
+ 577: 3.156e7, # year (calendar)
+ 723733: 1.0e-3, # millisecond
+ 842015: 1.0e-6, # microsecond
+ 838801: 1.0e-9, # nanosecond
+ 3902709: 1.0e-12, # picosecond
+ 1777507: 1.0e-15, # femtosecond
+ 2483628: 1.0e-18 # attosecond
+}
+
+def time_quantity_in_seconds(claim):
+ amount = None
+ if 'mainsnak' in claim:
+ if 'datavalue' in claim['mainsnak']:
+ quantity = claim['mainsnak']['datavalue']['value']
+ amount = float(quantity['amount'])
+ unit_uri = quantity['unit'] # Has form
http://www.wikidata.org/entity/Q577
+ unit_id = int(unit_uri.split('/')[-1].replace('Q',''))
+ amount *= time_units[unit_id]
+ return amount
--
To view, visit https://gerrit.wikimedia.org/r/245591
To unsubscribe, visit https://gerrit.wikimedia.org/r/settings
Gerrit-MessageType: newchange
Gerrit-Change-Id: I0a3fe4c20f6442f951cd54a1024334283dd9aaeb
Gerrit-PatchSet: 1
Gerrit-Project: labs/tools/ptable
Gerrit-Branch: master
Gerrit-Owner: arthurpsm...@gmail.com
_______________________________________________
MediaWiki-commits mailing list
MediaWiki-commits@lists.wikimedia.org
https://lists.wikimedia.org/mailman/listinfo/mediawiki-commits
